Hi, Firstly, I think you will need to put biojava.jar into your classpath rather than java.jar.
Seccondly, you are running the class PdbToXMLConverter. Did you compile this yourself? If you did, I think you may have a package statement on the first non-comment, non-empty line that says: package org.biojava.bio.program; To make the program run, you eiter need the .class file from compiling this to be in a directory org/biojava/bio/program (relative to your classpath) and type java org.biojava.bio.program.PdbToXMLConverter 1FS1.pdb, or you need to remove the package line from the file. If you did not compile the application yourself, you will probably find that putting biojava.jar into your path and typing the new command-line works. If you have any more trouble, drop us a line. Matthew --- jon portuondo murguiondo <[EMAIL PROTECTED]> wrote: > Hello, > I have a problem when I try to execute the program > PdbToXML. I think the problem is I don't have the > java.jar library, but where I can find it? (I have > linux). I would be very pleased you could help me. > The errors are the following (if you think the > problem is not the java.jar library, tell me > please!): > [jon@diana ~]$ java PdbToXMLConverter 1FS1.pdb > Exception in thread "main" > java.lang.NoClassDefFoundError: PdbToXMLConverter > (wrong name: > org/biojava/bio/program/PdbToXMLConverter) > at java.lang.ClassLoader.defineClass0(Native > Method) > at > java.lang.ClassLoader.defineClass(ClassLoader.java:502) > at > java.security.SecureClassLoader.defineClass(SecureClassLoader.java:123) > at > java.net.URLClassLoader.defineClass(URLClassLoader.java:250) > at > java.net.URLClassLoader.access$100(URLClassLoader.java:54) > at > java.net.URLClassLoader$1.run(URLClassLoader.java:193) > at > java.security.AccessController.doPrivileged(Native > Method) > at > java.net.URLClassLoader.findClass(URLClassLoader.java:186) > at > java.lang.ClassLoader.loadClass(ClassLoader.java:299) > at > sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:265) > at > java.lang.ClassLoader.loadClass(ClassLoader.java:255) > at > java.lang.ClassLoader.loadClassInternal(ClassLoader.java:315) > > _______________________________________________ > Biojava-l mailing list - [EMAIL PROTECTED] > http://biojava.org/mailman/listinfo/biojava-l __________________________________________________ Do You Yahoo!? Everything you'll ever need on one web page from News and Sport to Email and Music Charts http://uk.my.yahoo.com _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
